Proteochemometrics modeling for prediction of the interactions between caspase isoforms and their inhibitors.

Caspases (cysteine-aspartic proteases) play critical roles in inflammation and the programming of cell death in the form of necroptosis, apoptosis, and pyroptosis. The name of these enzymes has been chosen in accordance with their cysteine protease activity. They act as cysteines in nucleophilically active sites to attack and cleave target proteins in the aspartic acid and amino acid C-terminal. Based on the substrate's structure and the specificity, the physiological activity of caspases is divided. However, in apoptosis, the division of caspases into initiating caspases (caspase 2, 8, 9, and 10) and executive caspases (caspase 3, 6, and 7) is essential. The present study aimed to perform Proteochemometrics Modeling to generalize the data on caspases, which could predict ligand and protein interactions. In this study, we employed protein and ligand descriptors. Moreover, protein descriptors were computed using the Protr R package, while PADEL-Descriptor was employed for the computation of ligand descriptors. In addition, NCA (Neighborhood Component Analyses) was used for descriptor selection, and SVR, decision tree, and ensemble methods were utilized for the proteochemometrics modeling. This study shows that the ensemble model demonstrates superior performance compared with other models in terms of R2, Q2, and RMSE criteria.

A combined Fisher and Laplacian score for feature selection in QSAR based drug design using compounds with known and unknown activities.

Quantitative structure-activity relationship (QSAR) is an effective computational technique for drug design that relates the chemical structures of compounds to their biological activities. Feature selection is an important step in QSAR based drug design to select the most relevant descriptors. One of the most popular feature selection methods for classification problems is Fisher score which aim is to minimize the within-class distance and maximize the between-class distance. In this study, the properties of Fisher criterion were extended for QSAR models to define the new distance metrics based on the continuous activity values of compounds with known activities. Then, a semi-supervised feature selection method was proposed based on the combination of Fisher and Laplacian criteria which exploits both compounds with known and unknown activities to select the relevant descriptors. To demonstrate the efficiency of the proposed semi-supervised feature selection method in selecting the relevant descriptors, we applied the method and other feature selection methods on three QSAR data sets such as serine/threonine-protein kinase PLK3 inhibitors, ROCK inhibitors and phenol compounds. The results demonstrated that the QSAR models built on the selected descriptors by the proposed semi-supervised method have better performance than other models. This indicates the efficiency of the proposed method in selecting the relevant descriptors using the compounds with known and unknown activities. The results of this study showed that the compounds with known and unknown activities can be helpful to improve the performance of the combined Fisher and Laplacian based feature selection methods.

Health-aware food recommendation system with dual attention in heterogeneous graphs.

Recommender systems (RS) have been increasingly applied to food and health. However, challenges still remain, including the effective incorporation of heterogeneous information and the discovery of meaningful relationships among entities in the context of food and health recommendations. To address these challenges, we propose a novel framework, the Health-aware Food Recommendation System with Dual Attention in Heterogeneous Graphs (HFRS-DA), for unsupervised representation learning on heterogeneous graph-structured data. HFRS-DA utilizes an attention technique to reconstruct node features and edges and employs a dual hierarchical attention mechanism for enhanced unsupervised learning of attributed graph representations. HFRS-DA addresses the challenge of effectively leveraging the heterogeneous information in the graph and discovering meaningful semantic relationships between entities. The framework analyses recipe components and their neighbours in the heterogeneous graph and can discover popular and healthy recipes, thereby promoting healthy eating habits. We compare HFRS-DA using the Allrecipes dataset and find that it outperforms all the related methods from the literature. Our study demonstrates that HFRS-DA enhances the unsupervised learning of attributed graph representations, which is important in scenarios where labelled data is scarce or unavailable. HFRS-DA can generate node embeddings for unused data effectively, enabling both inductive and transductive learning.

Drug-target interaction prediction using reliable negative samples and effective feature selection methods.

Machine learning-based approaches in the field of drug discovery have dramatically reduced the time and cost of the laboratory process of detecting potential drug-target interactions (DTIs). Standard binary classifiers require both positive and negative samples in the training and validation phases. One of the major challenges in the DTI context is the lack of access to non-interacting pairs as negative samples in the learning process. Many recent studies in this field have randomly selected negative samples from unlabeled drug-target pairs. Therefore, due to the probability of the presence of unknown positive samples in a set considered as negative samples, the model results may be affected and appear with a high rate of false positive. In this study, an algorithm called Reliable Non-Interacting Drug-Target Pairs (RNIDTP) is proposed to select reliable negative samples and an efficient algorithm to select relevant features for drug-target interaction prediction. To validate the performance of the proposed RNIDTP algorithm in the selection of negative samples, a benchmark drug-target interactions dataset is used. The results demonstrate the superiority of the proposed algorithm compared with other algorithms in most cases. The results also indicate that by using an appropriate algorithm for the selection of negative samples, the performance of the learning process is significantly increased compared to random selection.